In my experience this expression is almost always used ironically. When somebody proposes a dubious course of action, justifying it with the claim that the end justifies the means, an onlooker might dryly observe, "You can't make an omelet without breaking eggs." As mblase pointed out, the original use of the expression was to rationalize actions that were less than noble, to say the least. I think this comes through in the standard usage; the speaker is reminding the listener that this logic has been used by sketchy people throughout history to justify attrocities.

In fact, the few nonironic usages I can think of for this expression have generally come from Hollywood bad guys, and the intent there seems to be to make us hate them for their ruthlessness and ethical bankruptcy. Has anyone actually seen this expression used by a real person in an non-self conscious sense? I don't think I've ever seen it in live usage.